6D07: Chromobox protein homolog 1

Crystal structure of the complex between human chromobox homolog 1 (CBX1) and H3K9me3 peptide. Determined by X-ray diffraction at 2.1 Å resolution. Released 10 Apr 2019.

Method: X-ray diffraction
Resolution: 2.1 Å
Organism: Homo sapiens
Chains: 4
Atoms: 1,113
Mol. weight: 16.3 kDa
Released: 10 Apr 2019

Explore 6D07 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6D07 contains 7 α-helices and 12 β-strands across 4 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 3 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	1
β-strand	5-14	10	2
β-strand	17-24	8	2
α-helix	29-31	3
β-strand	33-36	4	2
α-helix	37-39	3
β-strand	40-41	2	1
α-helix	43-53	11

Chain B: 3 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	3
β-strand	5-14	10	4
β-strand	17-24	8	4
α-helix	29-31	3
β-strand	33-36	4	4
α-helix	37-39	3
β-strand	40-41	2	3
α-helix	43-50	8

Chain C: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	6-8	3	1
α-helix	9-11	3

Chain D: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	6-8	3	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Chromobox protein homolog 1	A, B	protein	55	Homo sapiens	P83916 (AlphaFold model)
Histone H3.1	C, D	protein	16	Homo sapiens	P68431 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6D07_1 Chromobox protein homolog 1 (chains A, B)
GEYVVEKVLDRRVVKGKVEYLLKWKGFSDEDNTWEPEENLDCPDLIAEFLQSQKT

Sequence of entity 2 (C, D), FASTA

>6D07_2 Histone H3.1 (chains C, D)
ARTKQTARKSTGGKAX

Primary citation

Engineering Methyllysine Writers and Readers for Allele-Specific Regulation of Protein-Protein Interactions. Arora, S., Horne, W.S., Islam, K. J Am Chem Soc (2019) 141:15466-15470. DOI 10.1021/jacs.9b05725 · PubMed

Other PDB entries of the same protein (UniProt P83916 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2FMM 1.8 Å, Crystal Structure of EMSY-HP1 complex
3F2U 1.8 Å, Crystal structure of human chromobox homolog 1 (CBX1)
5T1G 1.9 Å, chromo shadow domain of CBX1 in complex with a histone peptide
3Q6S 1.93 Å, The crystal structure of the heterochromatin protein 1 beta chromoshadow domain…
6D08 2.1 Å, Crystal structure of an engineered bump-hole complex of mutant human chromobox homolog 1…

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